S4E24 · Gethsemane

The episode opens in medias res to police investigating a dead body in the apartment of FBI agent Fox Mulder (David Duchovny). Dana Scully (Gillian Anderson) confirms the unseen body's identity and leaves. She subsequently appears before an FBI panel led by Section Chief Scott Blevins (Charles Cioffi), reviewing her work with Mulder on the X-Files.

In Canada 's Saint Elias Mountains, a frozen extraterrestrial body is discovered by an expedition team. Professor Arlinsky, the team's leader, sends ice core samples containing presumably alien DNA to Mulder. Scully has the samples tested and confirms the DNA's non-terrestrial origin, but is attacked by a man who steals the samples. Scully learns that her attacker is Michael Kritschgau (John Finn), a Defense Department employee. When she tracks down Kritschgau and holds him at gunpoint, he reveals that he might be killed.

Meanwhile, Arlinsky returns to the mountains with Mulder, but they find that most of the expedition members have been shot dead. The sole survivor is a man named Babcock, who reveals that he has saved the alien corpse from theft by burying it. Together, the three men bring the corpse to the United States. There, Mulder and Arlinsky perform an autopsy on the corpse, believing it belongs to a genuine extraterrestrial. After Mulder leaves to meet with Scully, a mysterious assassin, Scott Ostelhoff, arrives and kills both Babcock and Arlinsky.

Scully introduces Mulder to Kritschgau, who claims that everything Mulder thinks he knows about aliens is a lie. He tells him that his sister's abduction was fabricated, that all evidence of alien biology are merely scientific anomalies, and that the alien body he has just examined was fake. Kritschgau claims that the entire alien mythos is a hoax perpetrated by the U.S. government as a cover for the activities of the military–industrial complex. Mulder dismisses these claims.

Mulder finds Arlinsky and Babcock dead, with the alien body missing. Scully tells him Kritschgau told her that she was given cancer to make him believe. Mulder, distraught, sits in his apartment watching a conference about extraterrestrial life on television. The narrative returns to the present, where Scully reveals to the panel that Mulder died the previous night of an apparent self-inflicted gunshot wound to the head.